rs77009095
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_003664.5(AP3B1):c.1969-10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0692 in 1,593,932 control chromosomes in the GnomAD database, including 4,256 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_003664.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AP3B1 | NM_003664.5 | c.1969-10G>A | intron_variant | Intron 17 of 26 | ENST00000255194.11 | NP_003655.3 | ||
AP3B1 | NM_001271769.2 | c.1822-10G>A | intron_variant | Intron 17 of 26 | NP_001258698.1 | |||
AP3B1 | NM_001410752.1 | c.1969-10G>A | intron_variant | Intron 17 of 22 | NP_001397681.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0531 AC: 8077AN: 152090Hom.: 327 Cov.: 32
GnomAD3 exomes AF: 0.0594 AC: 14856AN: 250254Hom.: 543 AF XY: 0.0619 AC XY: 8377AN XY: 135408
GnomAD4 exome AF: 0.0709 AC: 102280AN: 1441724Hom.: 3930 Cov.: 27 AF XY: 0.0711 AC XY: 51103AN XY: 718722
GnomAD4 genome AF: 0.0530 AC: 8073AN: 152208Hom.: 326 Cov.: 32 AF XY: 0.0529 AC XY: 3935AN XY: 74414
ClinVar
Submissions by phenotype
not specified Benign:2
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1969-10G>A in intron 17 of AP3B1: This variant is not expected to have clinical significance because it has been identified in 7.5% (642/8600) of European Ameri can chromosomes from a broad population by the NHLBI Exome Sequencing Project (h ttp://evs.gs.washington.edu/EVS; dbSNP rs77009095). -
not provided Benign:2
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Hermansky-Pudlak syndrome 2 Benign:1
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Hermansky-Pudlak syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at